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homogenise peptidoform strings in DDA result files #446

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merged 3 commits into from
Nov 22, 2024
Merged

homogenise peptidoform strings in DDA result files #446

merged 3 commits into from
Nov 22, 2024

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Cajac102
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2 minor changes:

  1. fix regex for modification detection in sage and FragPipe parsing (the old one included the square brackets in the match group, and therefore they did not match to the modifications in the .toml)
  2. parse charges from AlphaPept output to int

@Cajac102 Cajac102 linked an issue Nov 21, 2024 that may be closed by this pull request
Replace mass shifts in peptide proforma strings during FragPipe and Sage parsing with modification names #444
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@RobbinBouwmeester RobbinBouwmeester merged commit 1e1710e into main Nov 22, 2024
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@RobbinBouwmeester RobbinBouwmeester deleted the 444-replace-mass-shifts-in-peptide-proforma-strings-during-fragpipe-and-sage-parsing-with-modification-names branch November 22, 2024 11:47
@Cajac102 Cajac102 restored the 444-replace-mass-shifts-in-peptide-proforma-strings-during-fragpipe-and-sage-parsing-with-modification-names branch November 22, 2024 12:42
@Cajac102
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Another issue: N-terminal modifications are reported as internal modifications on the first position by i2masschroq and PEAKS (e.g. "A[MOD:00394]AAAAAAGDSDSWDADAFSVEDPVRK" instead of [MOD:00394]-AA....").

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@RobbinBouwmeester RobbinBouwmeester RobbinBouwmeester approved these changes

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Replace mass shifts in peptide proforma strings during FragPipe and Sage parsing with modification names
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@Cajac102 @RobbinBouwmeester